[Bioc-devel] Error in NSBS
On Fri, Dec 11, 2015 at 2:02 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:
Hi, On 12/11/2015 12:42 PM, Krithika Bhuvaneshwar [kb472 at georgetown.edu] wrote:
Thank you for your email. I did fix the issue. The problem was with GenomicRanges in the DESCRIPTION/NAMESPACE file of the package. Initially I listed it in the "imports" section of the DESCRIPTION file, and it looks like the vignette was not picking it up when I tried to build it. So I put it in "depends" section. I also made sure import(GenomicRanges) was added to NAMESPACE. That seemed to fix the issue.
I'm guessing that it was adding import(GenomicRanges) to NAMESPACE that fixed the issue. You should never have to list the package in Depends to fix symbol resolution.
Good to know. I'm putting this back on the list where you originally posted this so the other the developers know that you've addressed the issue and they don't need to spend time trying to help you with this. Cheers, H.
Thanks ! --Krithika ------------------------------------------------------------------------------ Ms. Krithika Bhuvaneshwar Bioinformatician/Data Manager Innovation Center for Biomedical Informatics (ICBI), Georgetown University Medical Center, Washington, DC Email: kb472 at georgetown.edu <mailto:kb472 at georgetown.edu> ; krithika.gu at gmail.com <mailto:krithika.gu at gmail.com> Phone: 202-687-6850; Fax: 202-687-5011 http://icbi.georgetown.edu/ ------------------------------------------------------------------------------- On Fri, Dec 11, 2015 at 3:38 PM, Herv? Pag?s <hpages at fredhutch.org <mailto:hpages at fredhutch.org>> wrote: Hi Krithika, NSBS() is the internal helper defined in the S4Vectors package that takes care of checking and normalizing the supplied subscript when one tries to subset a Vector derivative (e.g. an Rle, Hits, IRanges, GRanges, GRangesList, etc...). For example:
> IRanges(1:26, 50, names=letters)[LETTERS]
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
:
subscript contains invalid names
It's just saying that the subscript 'i' contains names that are not
valid.
So it seems that in your case a subsetting operation that happens
in run.cin.chr() works just fine when you run run.cin.chr()
interactively but not in the context of knitPDF.
It's hard to know why without having more details.
Could you please run R CMD Stangle on your Rmarkdown file? That will
produce a .R file. Then start R and source this .R file with
source("file_produced_by_R_CMD_Stangle.R" , echo=TRUE).
Then please report the full output you get as well as the output of
sessionInfo() (call this after the source() command terminates).
Please use sessionInfo(), not session_info().
Thanks,
H.
On 12/10/2015 09:27 PM, Krithika Bhuvaneshwar [kb472 at georgetown.edu
<mailto:kb472 at georgetown.edu>] wrote:
Hello,
I am working on creating a package, and have come across an issue.
I have some R code in the "R" folder that works just fine when I
test it.
The code contains a function accepts a GRangesList as input.
I call the function from my Rmarkdown file in the "vignette"
folder. When I
test the "code chunk" from the Rmd file, the function works just
fine. But
when I try to "knitPDF", it gives this error
Error in NSBS(i, x, exact = exact, upperBoundIsStrict =
!allow.append) :
subscript contains invalid names
Calls: <Anonymous> ... [ -> normalizeSingleBracketSubscript ->
NSBS -> NSBS
The code is like this:
data("grl")
run.cin.chr(grl.seg = grl) #grl is the GRangesList input
Any help on how to fix this issue is much appreciated.
This is my session Info.
session_info()
Session info
-----------------------------------------------------------------------------------------
setting value
version R version 3.2.2 (2015-08-14)
system x86_64, darwin13.4.0
ui RStudio (0.99.489)
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2015-12-10
Packages
---------------------------------------------------------------------------------------------
package * version date source
acepack 1.3-3.3 2014-11-24 CRAN
(R 3.2.0)
affxparser 1.42.0 2015-10-14
Bioconductor
affyio 1.40.0 2015-10-14
Bioconductor
AnnotationDbi * 1.32.2 2015-12-09
Bioconductor
AnnotationHub * 2.2.2 2015-11-08
Bioconductor
Biobase * 2.30.0 2015-10-14
Bioconductor
BiocGenerics * 0.16.1 2015-11-06
Bioconductor
BiocInstaller 1.20.1 2015-11-18
Bioconductor
BiocParallel 1.4.0 2015-10-14
Bioconductor
biomaRt 2.26.1 2015-11-23
Bioconductor
Biostrings * 2.38.2 2015-11-21
Bioconductor
biovizBase * 1.18.0 2015-10-14
Bioconductor
bit 1.1-12 2014-04-09 CRAN
(R 3.2.0)
bitops 1.0-6 2013-08-17 CRAN
(R 3.2.0)
BSgenome 1.38.0 2015-10-14
Bioconductor
caTools 1.17.1 2014-09-10 CRAN
(R 3.2.0)
CINdex * 0.99.4 2015-12-10
Bioconductor
cluster 2.0.3 2015-07-21 CRAN
(R 3.2.2)
codetools 0.2-14 2015-07-15 CRAN
(R 3.2.2)
colorspace 1.2-6 2015-03-11 CRAN
(R 3.2.0)
DBI * 0.3.1 2014-09-24 CRAN
(R 3.2.0)
devtools * 1.9.1 2015-09-11 CRAN
(R 3.2.0)
dichromat 2.0-0 2013-01-24 CRAN
(R 3.2.0)
digest 0.6.8 2014-12-31 CRAN
(R 3.2.0)
ff 2.2-13 2014-04-09 CRAN
(R 3.2.0)
foreach 1.4.3 2015-10-13 CRAN
(R 3.2.0)
foreign 0.8-66 2015-08-19 CRAN
(R 3.2.0)
Formula 1.2-1 2015-04-07 CRAN
(R 3.2.0)
futile.logger 1.4.1 2015-04-20 CRAN
(R 3.2.0)
futile.options 1.0.0 2010-04-06 CRAN
(R 3.2.0)
gdata 2.17.0 2015-07-04 CRAN
(R 3.2.0)
GenomeInfoDb * 1.6.1 2015-11-03
Bioconductor
GenomicAlignments 1.6.1 2015-10-22
Bioconductor
GenomicFeatures * 1.22.6 2015-12-03
Bioconductor
GenomicRanges * 1.22.1 2015-11-06
Bioconductor
ggplot2 1.0.1 2015-03-17 CRAN
(R 3.2.0)
GO.db * 3.2.2 2015-11-12
Bioconductor
gplots 2.17.0 2015-05-02 CRAN
(R 3.2.0)
graph 1.48.0 2015-10-14
Bioconductor
gridExtra 2.0.0 2015-07-14 CRAN
(R 3.2.0)
gtable 0.1.2 2012-12-05 CRAN
(R 3.2.0)
gtools 3.5.0 2015-05-29 CRAN
(R 3.2.0)
Hmisc 3.17-0 2015-09-21 CRAN
(R 3.2.0)
Homo.sapiens * 1.3.1 2015-12-09
Bioconductor
htmltools 0.2.6 2014-09-08 CRAN
(R 3.2.0)
httpuv 1.3.3 2015-08-04 CRAN
(R 3.2.0)
httr 1.0.0 2015-06-25 CRAN
(R 3.2.0)
interactiveDisplayBase 1.8.0 2015-10-14
Bioconductor
IRanges * 2.4.5 2015-12-08
Bioconductor
iterators 1.0.8 2015-10-13 CRAN
(R 3.2.0)
KernSmooth 2.23-15 2015-06-29 CRAN
(R 3.2.2)
knitr * 1.11 2015-08-14 CRAN
(R 3.2.2)
lambda.r 1.1.7 2015-03-20 CRAN
(R 3.2.0)
lattice 0.20-33 2015-07-14 CRAN
(R 3.2.2)
latticeExtra 0.6-26 2013-08-15 CRAN
(R 3.2.0)
magrittr 1.5 2014-11-22 CRAN
(R 3.2.0)
MASS 7.3-45 2015-11-10 CRAN
(R 3.2.2)
memoise 0.2.1 2014-04-22 CRAN
(R 3.2.0)
mime 0.4 2015-09-03 CRAN
(R 3.2.0)
munsell 0.4.2 2013-07-11 CRAN
(R 3.2.0)
nnet 7.3-11 2015-08-30 CRAN
(R 3.2.0)
oligo * 1.34.0 2015-10-14
Bioconductor
oligoClasses * 1.32.0 2015-10-14
Bioconductor
org.Hs.eg.db * 3.2.3 2015-12-09
Bioconductor
OrganismDbi * 1.12.0 2015-10-14
Bioconductor
pd.genomewidesnp.6 * 3.14.1 2015-11-30
Bioconductor
plyr 1.8.3 2015-06-12 CRAN
(R 3.2.0)
preprocessCore 1.32.0 2015-10-14
Bioconductor
proto 0.3-10 2012-12-22 CRAN
(R 3.2.0)
R6 2.1.1 2015-08-19 CRAN
(R 3.2.0)
RBGL 1.46.0 2015-10-14
Bioconductor
RColorBrewer 1.1-2 2014-12-07 CRAN
(R 3.2.0)
Rcpp 0.12.2 2015-11-15 CRAN
(R 3.2.2)
RCurl 1.95-4.7 2015-06-30 CRAN
(R 3.2.0)
reshape2 1.4.1 2014-12-06 CRAN
(R 3.2.0)
rmarkdown 0.8.1 2015-10-10 CRAN
(R 3.2.2)
rpart 4.1-10 2015-06-29 CRAN
(R 3.2.2)
Rsamtools 1.22.0 2015-10-14
Bioconductor
RSQLite * 1.0.0 2014-10-25 CRAN
(R 3.2.0)
rtracklayer * 1.30.1 2015-10-22
Bioconductor
S4Vectors * 0.8.4 2015-12-08
Bioconductor
scales 0.3.0 2015-08-25 CRAN
(R 3.2.0)
shiny 0.12.2 2015-08-05 CRAN
(R 3.2.0)
som 0.3-5 2010-04-07 CRAN
(R 3.2.0)
stringi 1.0-1 2015-10-22 CRAN
(R 3.2.0)
stringr 1.0.0 2015-04-30 CRAN
(R 3.2.0)
SummarizedExperiment 1.0.1 2015-11-06
Bioconductor
survival 2.38-3 2015-07-02 CRAN
(R 3.2.2)
TxDb.Hsapiens.UCSC.hg18.knownGene * 3.2.2 2015-12-09
Bioconductor
TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2015-12-09
Bioconductor
VariantAnnotation 1.16.4 2015-12-09
Bioconductor
XML 3.98-1.3 2015-06-30 CRAN
(R 3.2.0)
xtable 1.8-0 2015-11-02 CRAN
(R 3.2.0)
XVector * 0.10.0 2015-10-14
Bioconductor
yaml 2.1.13 2014-06-12 CRAN
(R 3.2.0)
zlibbioc 1.16.0 2015-10-14
Bioconductor
Thanks,
--Krithika
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--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
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